Added test and updated request methods

.github/workflows/pytest-windows.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11"]
         os: [windows-latest]
 
     steps:

.github/workflows/pytest.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.11"]
+        python-version: ["3.8", "3.12"]
         os: [ubuntu-20.04]
 
     steps:

Makefile

@@ -5,7 +5,7 @@ run-coverage:
 	coverage run -m pytest
 
 html-report:
-	coverage html
+	coverage html --omit="*/test*"
 
 open-coverage:
 	cd htmlcov && google-chrome index.html

pephubclient/constants.py

@@ -4,10 +4,10 @@
 
 from pydantic import BaseModel, field_validator
 
-# PEPHUB_BASE_URL = os.getenv(
-#     "PEPHUB_BASE_URL", default="https://pephub-api.databio.org/"
-# )
-PEPHUB_BASE_URL = "http://0.0.0.0:8000/"
+PEPHUB_BASE_URL = os.getenv(
+    "PEPHUB_BASE_URL", default="https://pephub-api.databio.org/"
+)
+# PEPHUB_BASE_URL = "http://0.0.0.0:8000/"
 PEPHUB_PEP_API_BASE_URL = f"{PEPHUB_BASE_URL}api/v1/projects/"
 PEPHUB_PEP_SEARCH_URL = f"{PEPHUB_BASE_URL}api/v1/namespaces/{{namespace}}/projects"
 PEPHUB_PUSH_URL = f"{PEPHUB_BASE_URL}api/v1/namespaces/{{namespace}}/projects/json"

pephubclient/files_manager.py

@@ -6,7 +6,6 @@
 import yaml
 import zipfile
 
-from pephubclient.constants import RegistryPath
 from pephubclient.exceptions import PEPExistsError
 
 

pephubclient/models.py

@@ -1,5 +1,5 @@
 import datetime
-from typing import Optional, List
+from typing import Optional, List, Union
 
 from pydantic import BaseModel, Field, field_validator, ConfigDict
 from peppy.const import CONFIG_KEY, SUBSAMPLE_RAW_LIST_KEY, SAMPLE_RAW_DICT_KEY
@@ -43,6 +43,9 @@ class ProjectAnnotationModel(BaseModel):
     submission_date: datetime.datetime
     digest: str
     pep_schema: str
+    pop: bool = False
+    stars_number: Optional[int] = 0
+    forked_from: Optional[Union[str, None]] = None
 
 
 class SearchReturnModel(BaseModel):

pephubclient/modules/sample.py

@@ -42,12 +42,16 @@ def get(
         response = self.send_request(
             method="GET", url=url, headers=self.parse_header(self.__jwt_data)
         )
-        if response.status_code != ResponseStatusCodes.OK:
+        if response.status_code == ResponseStatusCodes.OK:
+            return self.decode_response(response, output_json=True)
+        if response.status_code == ResponseStatusCodes.NOT_EXIST:
+            raise ResponseError("Sample does not exist.")
+        elif response.status_code == ResponseStatusCodes.INTERNAL_ERROR:
+            raise ResponseError("Internal server error. Unexpected return value.")
+        else:
             raise ResponseError(
-                f"Sample does not exist, or Internal server error occurred."
+                f"Unexpected return value. Error: {response.status_code}"
             )
-        else:
-            return self.decode_response(response, output_json=True)
 
     def create(
         self,
@@ -93,9 +97,7 @@ def create(
             return None
 
         elif response.status_code == ResponseStatusCodes.NOT_EXIST:
-            raise ResponseError(
-                f"Project '{namespace}/{name}:{tag}' does not exist. Error: {response.status_code}"
-            )
+            raise ResponseError(f"Project '{namespace}/{name}:{tag}' does not exist.")
         elif response.status_code == ResponseStatusCodes.CONFLICT:
             raise ResponseError(
                 f"Sample '{sample_name}' already exists. Set overwrite to True to overwrite sample."

pephubclient/modules/view.py

@@ -8,6 +8,7 @@
     ResponseStatusCodes,
 )
 from pephubclient.exceptions import ResponseError
+from pephubclient.models import ProjectDict
 
 
 class PEPHubView(RequestManager):
@@ -52,6 +53,7 @@ def get(
             output = self.decode_response(response, output_json=True)
             if raw:
                 return output
+            output = ProjectDict(**output).model_dump(by_alias=True)
             return peppy.Project.from_dict(output)
         elif response.status_code == ResponseStatusCodes.NOT_EXIST:
             raise ResponseError("View does not exist, or you are unauthorized.")
@@ -213,7 +215,7 @@ def remove_sample(
             )
         elif response.status_code == ResponseStatusCodes.UNAUTHORIZED:
             raise ResponseError(
-                f"You are unauthorized to remove this sample from the view."
+                "You are unauthorized to remove this sample from the view."
             )
         else:
             raise ResponseError(

pephubclient/pephubclient.py

@@ -1,10 +1,8 @@
-import json
 from typing import NoReturn, Optional, Literal
 from typing_extensions import deprecated
 
 import peppy
 from peppy.const import NAME_KEY
-import requests
 import urllib3
 from pydantic import ValidationError
 from ubiquerg import parse_registry_path
@@ -107,7 +105,6 @@ def load_project(
         :param query_param: query parameters used in get request
         :return Project: peppy project.
         """
-        jwt = FilesManager.load_jwt_data_from_file(PATH_TO_FILE_WITH_JWT)
         raw_pep = self.load_raw_pep(project_registry_path, query_param)
         peppy_project = peppy.Project().from_dict(raw_pep)
         return peppy_project
@@ -250,11 +247,11 @@ def find_project(
             cookies=None,
         )
         if pephub_response.status_code == ResponseStatusCodes.OK:
-            decoded_response = self._handle_pephub_response(pephub_response)
+            decoded_response = self.decode_response(pephub_response, output_json=True)
             project_list = []
-            for project_found in json.loads(decoded_response)["items"]:
+            for project_found in decoded_response["items"]:
                 project_list.append(ProjectAnnotationModel(**project_found))
-            return SearchReturnModel(**json.loads(decoded_response))
+            return SearchReturnModel(**decoded_response)
 
     @deprecated("This method is deprecated. Use load_raw_pep instead.")
     def _load_raw_pep(
@@ -297,8 +294,8 @@ def load_raw_pep(
             cookies=None,
         )
         if pephub_response.status_code == ResponseStatusCodes.OK:
-            decoded_response = self._handle_pephub_response(pephub_response)
-            correct_proj_dict = ProjectDict(**json.loads(decoded_response))
+            decoded_response = self.decode_response(pephub_response, output_json=True)
+            correct_proj_dict = ProjectDict(**decoded_response)
 
             # This step is necessary because of this issue: https://github.com/pepkit/pephub/issues/124
             return correct_proj_dict.model_dump(by_alias=True)
@@ -362,15 +359,3 @@ def _build_push_request_url(namespace: str) -> str:
         :return: url string
         """
         return PEPHUB_PUSH_URL.format(namespace=namespace)
-
-    @staticmethod
-    def _handle_pephub_response(pephub_response: requests.Response):
-        """
-        Check pephub response
-        """
-        decoded_response = PEPHubClient.decode_response(pephub_response)
-
-        if pephub_response.status_code != ResponseStatusCodes.OK:
-            raise ResponseError(message=json.loads(decoded_response).get("detail"))
-
-        return decoded_response

setup.py

@@ -43,6 +43,7 @@ def read_reqs(reqs_name):
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],
     keywords="project, bioinformatics, metadata",

tests/conftest.py

@@ -1,5 +1,3 @@
-import json
-
 import pytest
 
 from pephubclient.pephub_oauth.models import InitializeDeviceCodeResponse
@@ -29,7 +27,7 @@ def test_raw_pep_return():
             {"time": "0", "file_path": "source1", "sample_name": "frog_0h"},
         ],
     }
-    return json.dumps(sample_prj)
+    return sample_prj
 
 
 @pytest.fixture

tests/test_manual.py

@@ -0,0 +1,101 @@
+from pephubclient.pephubclient import PEPHubClient
+import pytest
+
+
+@pytest.mark.skip(reason="Manual test")
+class TestViewsManual:
+
+    def test_get(self):
+        ff = PEPHubClient().view.get(
+            "databio",
+            "bedset1",
+            "default",
+            "test_view",
+        )
+        print(ff)
+
+    def test_create(self):
+        PEPHubClient().view.create(
+            "databio",
+            "bedset1",
+            "default",
+            "test_view",
+            sample_list=["orange", "grape1", "apple1"],
+        )
+
+    def test_delete(self):
+        PEPHubClient().view.delete(
+            "databio",
+            "bedset1",
+            "default",
+            "test_view",
+        )
+
+    def test_add_sample(self):
+        PEPHubClient().view.add_sample(
+            "databio",
+            "bedset1",
+            "default",
+            "test_view",
+            "name",
+        )
+
+    def test_delete_sample(self):
+        PEPHubClient().view.remove_sample(
+            "databio",
+            "bedset1",
+            "default",
+            "test_view",
+            "name",
+        )
+
+
+@pytest.mark.skip(reason="Manual test")
+class TestSamplesManual:
+    def test_manual(self):
+        ff = PEPHubClient().sample.get(
+            "databio",
+            "bedset1",
+            "default",
+            "grape1",
+        )
+        ff
+
+    def test_update(self):
+        ff = PEPHubClient().sample.get(
+            "databio",
+            "bedset1",
+            "default",
+            "newf",
+        )
+        ff.update({"shefflab": "test1"})
+        ff["sample_type"] = "new_type"
+        PEPHubClient().sample.update(
+            "databio",
+            "bedset1",
+            "default",
+            "newf",
+            sample_dict=ff,
+        )
+
+    def test_add(self):
+        ff = {
+            "genome": "phc_test1",
+            "sample_type": "phc_test",
+        }
+        PEPHubClient().sample.create(
+            "databio",
+            "bedset1",
+            "default",
+            "new_2222",
+            overwrite=False,
+            sample_dict=ff,
+        )
+
+    def test_delete(self):
+        PEPHubClient().sample.remove(
+            "databio",
+            "bedset1",
+            "default",
+            "new_2222",
+        )